If their populations are being reduced, there will be fewer animals to suffer and I'd guess less overall suffering as a result. If you think they have overall bad lives or lives worth preventing, this would better, not worse.

And I don't think there's any feasible plan or path to improve their welfare on a similarly large scale, unlike for impoverished humans. Furthermore, the small and populous prey fish tend to have high mortality rates and short lives, which is a reason to believe their average welfare is negative (although possibly defeasible) that doesn't apply to impoverished humans.

The author's point about humanity's tendency towards scope insensitivity when considering animal issues is completely correct.

However, the article's claim seems to accept as a given that the reduction of wild animal populations due to human activity is bad for wild animal welfare. That claim is far from settled. Brian Tomasik argues (in my opinion, somewhat persuasively) that the pain of a wild animal's death, especially for a short-lived animal such as a bristlemouth fish, often overshadows the happiness of their life.

That said, it's great to see vegans express concern for the feelings of wild animals, and rightly point out that the magnitude of human activity on wild animal welfare is huge, for better or worse.